rs7834765

Variant names:

• chr8-121263666-G-T
• rs7834765
• ENST00000784704.1:n.101+14652G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000784704.1(ENSG00000302156):​n.101+14652G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,726 control chromosomes in the GnomAD database, including 8,507 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8507 hom., cov: 31)
• Consequence: ENSG00000302156 ENST00000784704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 9 publications found

Genes affected

ENSG00000302156 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302156	ENST00000784704.1	n.101+14652G>T		intron_variant	Intron 1 of 4
ENSG00000302156	ENST00000784705.1	n.154+14652G>T		intron_variant	Intron 2 of 2
ENSG00000302156	ENST00000784706.1	n.204+14652G>T		intron_variant	Intron 3 of 3
ENSG00000302156	ENST00000784707.1	n.101+14652G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48349 AN: 151608 Hom.: 8489 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.310

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.319 AC: 48422 AN: 151726 Hom.: 8507 Cov.: 31 AF XY: 0.326 AC XY: 24177 AN XY: 74124

African (AFR) AF: 0.395 AC: 16319 AN: 41360

American (AMR) AF: 0.427 AC: 6512 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3464

East Asian (EAS) AF: 0.546 AC: 2796 AN: 5120

South Asian (SAS) AF: 0.410 AC: 1970 AN: 4800

European-Finnish (FIN) AF: 0.308 AC: 3239 AN: 10520

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15835 AN: 67898

Other (OTH) AF: 0.314 AC: 662 AN: 2108

Alfa AF: 0.300 Hom.: 2312

Bravo AF: 0.329

Asia WGS AF: 0.477 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.31
PhyloP100		-0.92

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7834765; hg19: chr8-122275906;